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Human Immunology xxx (2016) xxx–xxx

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PTPN22 polymorphisms, but not R620W, were associated
with the genetic susceptibility of systemic lupus erythematosus
and rheumatoid arthritis in a Chinese Han population
Liang Tang a,c, Yan Wang a,c, Shui Zheng d, Meihua Bao a,c, Qingsong Zhang a,c, Jianming Li b,a,⇑
a
Department of Human Anatomy, Histology and Embryology, Institute of Neuroscience, Changsha Medical University, Changsha, PR China
b
Xiangya Hospital, Central South University, Changsha, PR China
c
School of Basic Medical Science, Changsha Medical University, Changsha, PR China
d
Key Laboratory for Fertility Regulation and Birth Health of Minority Nationalities of Yunnan Province, Judicial Expertise Center, Yunnan Population and Family Planning
Research Institute, Kunming, PR China

a r t i c l e i n f o a b s t r a c t

Article history: Objectives: The present study aimed to detect a possible association between PTPN22 gene polymor-
Received 8 October 2015 phisms and rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) in a Chinese Han popula-
Revised 18 January 2016 tion.
Accepted 28 April 2016
Methods: 7 PTPN22 SNPs were genotyped in 358 patients with RA and 713 patients with SLE, as well as
Available online xxxx
564 RA controls and 672 SLE controls by Restriction Fragment Length Polymorphism (RFLP). Association
analyses were conducted on the whole data set. Significant relationships were also examined between
Keywords:
clinical features and SNPs for both RA and SLE.
Protein tyrosine phosphatase nonreceptor
22 (PTPN22)
Results: Rs2476601 was lack of polymorphism with a 60.1% frequency in both SLE and RA patients and
Rheumatoid arthritis (RA) healthy controls in our study. The two SNPs rs1217414 and rs3811021 of PTPN22 shown strong associ-
Systemic lupus erythematosus (SLE) ation with both SLE (rs1217414T: padj = 6.07e!004, OR = 0.57; rs3811021C: padj = 4.68e!005,
Single nucleotide polymorphisms (SNPs) OR = 0.65) and RA (rs1217414T: padj = 2.01e!008, OR = 0.26; rs3811021C: padj = 0.028, OR = 0.70). And
Chinese Han the rs3765598 revealed a strong risk factor for SLE (p = 9.38e!009, padj = 6.57e!008, OR = 1.93), but
not for RA (p = 0.48, OR = 1.12). Moreover, protective haplotype ACTTC in RA (p = 7.73e!016, padj =
5.51!015, OR[95%CI] = 0.02[0.002–0.10]) and SLE (p = 8.29e!018, padj = 5.80e!017, OR[95%CI] = 0.11
[0.06–0.21]) were observed. In addition, the distribution of risk haplotypes ACGTC and GCTTT in RA
(ACGTC: p = 0.0006, padj = 0.004, OR[95%CI] = 1.85[1.29–2.63]; GCTTT: p = 2.62e!005, padj = 1.85e!004,
OR[95%CI] = 2.40[1.57–3.65]) and SLE (ACGTC: p = 0.0006, padj = 0.004, OR[95%CI] = 1.85[1.29–2.63];
ACGTC: p = 7.74e!011, padj = 6.81e!010, OR[95%CI] = 2.21[1.12–3.34]; GCTTT: p = 2.40[1.57–3.65],
padj = 2.26e!006, OR[95%CI] = 2.64[1.79–3.87]) were significant different from that in controls.
Furthermore, significant association was observed between the PTPN22 rs3765598 and antinuclear anti-
bodies 1 (ANA1) in SLE.
Conclusions: Our data provide strong evidence that the rs1217414 and rs3811021 in PTPN22 gene might
be common protective factors contributed to SLE and RA susceptibility in the Chinese Han population.
While, the rs3765598 might increase the genetic susceptibility of SLE, but not RA.
! 2016 Published by Elsevier Inc. on behalf of American Society for Histocompatibility and Immunoge-
netics.

1. Introduction autoimmune disorders that were thought to be caused by complex
interaction of multiple susceptibility genes and environmental fac-
Rheumatoid arthritis (RA [MIM 180300]) and systemic lupus tors and affects approximately 0.32% (1% in Caucasian) and 0.1%
erythematosus (SLE [MIM 152700]) are common complex (0.05% in Caucasian) of the Chinese population respectively [1].
Familiar and twins studies have provided robust evidence for the
⇑ Corresponding author at: Department of Human Anatomy, Histology and
role of genetic factors in these diseases [2,3]. It is becoming evident
Embryology, Institute of Neuroscience, Changsha Medical University, Changsha that systemic autoimmune diseases, including RA and SLE, share
410219, PR China. common genetic causative factors in populations of different eth-
E-mail address: ljming0901@sina.com (J. Li). nic or racial origin. The involvement of major histocompatibility

http://dx.doi.org/10.1016/j.humimm.2016.04.021
0198-8859/! 2016 Published by Elsevier Inc. on behalf of American Society for Histocompatibility and Immunogenetics.

Please cite this article in press as: L. Tang et al., PTPN22 polymorphisms, but not R620W, were associated with the genetic susceptibility of systemic lupus
erythematosus and rheumatoid arthritis in a Chinese Han population, Hum. Immunol. (2016), http://dx.doi.org/10.1016/j.humimm.2016.04.021

Immunol.12 CRP (mg/l) 25 ± 12. a total of Graves’ disease [7].3 216 ± 18. However. non-MHC alleles were also required.5 "C/cycle for 40 s. dsDNA.% 506/679 (74. ANA. Subsequently. single strand DNA- described by Bottini et al. Genotype 2. IgA.2 ± 11.5 71 ± 15.4 ± 16.4 (16–80 years) 31. The restriction enzymes and sequencing primers for SNPs were listed in Table 1s. In the present study.4 dsDNA+.5%) 0/672(0%) Abbreviation: SLEDAI.7 ± 13. (2016). Tang et al. ment Length Polymorphism (RFLP) and 10% of the samples were ducted in Chinese Han population. SSB.5 18.org/10. rheuma. Standard Deviation.2 4.2%) 0/672(0%) IgA mg/dl 87.% 183/655 (27. observed a significant association between the same PTPN22 1236 unrelated control subjects who without the history of multi- R620W variant and rheumatoid arthritis (RA) [9]. cycles at 95 "C for 20 s. 0. these data provide com- pelling evidence for involvement of PTPN22 R620W in 2.1%) 0/672(0%) IgM mg/dl 168 ± 24. Clinical features autoimmune disorders including type I diabetes (T1D) [4].04.6 years) who met the Ameri- Recently.2.3. Moreover. such as erythrocyte sedimentation rate (ESR). The multiplex PCR were carried out on the ABI Veriti Ther- should be taken into account in the development of autoimmune mal Cycler (Applied Biosystems. http://dx. For the RA patient cohorts. Buffer(Takara). Korean and Japanese popula. then between the possible implications of PTPN22 polymorphisms for 4 "C forever. Changsha Medical University.% 252/683(36. But.3 mM dNTPs. butterfly erythema. 2.1%) 0/672(0%) IgG mg/dl 104 ± 19. urine protein. Anti-Sm antibody. This variant (R620W) results in a substitution 713 Patients (Male/female: 102/611.1016/j.0 mM Mg2+. RA and SLE and healthy controls. Pho. Tang et al.2 L. diseases such as RA and SLE in these populations. Please cite this article in press as: L. RA patients SLE patients Clinical characteristics Mean ± SD Healthy control Clinical characteristics Mean ± SD Healthy control Male/female 94/264 126/438 102/611 97/575 Age (years) 41. erythrocyte sedimentation rate.% 237/308 (76. sents for genetic analysis were obtained from all subjects or their Calculation power was obtained at the 0.doi.% 294/698 (42. and thus autoimmune disorders. which might suggest a new susceptible locus of Inc. we aim selected at random to perform repeat assays as genotyping quality to ascertain whether the PTPN22 polymorphisms were etiologically control. A combination of 7 informative PTPN22 functional or tagging Interestingly. Sm. All participants were Chinese Han in origin. 10 PTPN22 gene in autoimmune diseases in this population. rheumatoid factor.27%) 0/564(0%) Pro+.2016. Sequencer (Applied Biosystems).9 ± 13.2 ± 12.05 level of significance. Hum. binding protein (SSB) were also listed in Table 1. but not R620W. Arginine 620 can College of Rheumatology (The American Rheumatism Associa- Tryptophan (R620W)) in protein tyrosine phosphatase non. [8]. gender and age) Kyogoku et al. As reported in including 1 ll genomic DNA (contain 5–10 ng DNA).021 . Genomic DNA was extracted from tions. The association Medical University. Written informed con..% 1/358 (0.7 55. photaesthesia. SD. a functional polymorphism (rs2476601. antinuclear (T1D) in North American and Sardinian populations was first antibody (ANA). an intron SNP (rs1217414) was signifi.35%) 0/564(0%) But+. Furthermore. was reported to be significantly associated with multiple tor (RF) status was determined for all the patients.4 ANA+. Clinical features such as anti-Sm antibody between R620W variant of the PTPN22 gene and Type 1 diabetes (anti-Sm).7 ± 13. / Human Immunology xxx (2016) xxx–xxx complex (MHC) alleles is a piece of evidence that supports the guardians. 27 cycles at 95 "C for 20 s. Genotyping was conducted using Restriction Frag- susceptibility to both RA and SLE [12–14]. CRP. age: 36. antinuclear antibodies.humimm. Changsha (TCR) signaling. which encodes the lymphoid PTP affiliated hospital. 358 unrelated patients above hypothesis. Platelets.4 years) who in Arg620Trp that disrupts Lyp binding to Csk [8] and would fulfilled the American College of Rheumatology 1982 criteria for thereby result in loss of negative regulation of T cell receptor SLE [16] were recruited from the first affiliated hospital. 72 "C for there have been limited available studies exploring the association 30 s.).9%) 0/564(0%) Pho+. ribonucleoprotein (RNP).5 SLEDAI 18. Considering the important role of PTPN22 in the pathogene. (Male/female: 94/264. C-reactive protein toid arthritis (RA) [5]. 3. anti-double-stranded DNA (anti-dsDNA). the R620W was not polymorphic in the Asian SNPs (selected from previous study [11]) was genotyped in both populations including Chinese Han.5%) 0/672(0%) RF+. Table 1 Clinical characteristics of RA and SLE patients.31 ± 21. Hardy-Weinberg equilibrium (HWE) was tested in the cases and sha Medical University (CMUEC-12C0523). IgG. more variants except for R620W method.6 (18–74 years) 39. RF.9(19–82 years) ESR (mm/h) 33.44 ± 8. IgM were shown in Table 1. 55 "C for 30 s. Begovich et al. RNP. Cycling parameters were as follows: 95 "C for 2 min.7 ± 11.7%) 0/672(0%) HLA-B27+.% 12/358 (3.7 ± 11.9%) 0/672(0%) PLT ("103/lL) 294 ± 11. 672). 67 "C !0. peripheral leukocytes using the standard phenol–chloroform sis of autoimmune diseases.6 SSB+.7 ± 13.% 406/547 (74.% 139/647 (21. Pro. And none was con. controls using a classic chi-square test with 1 degree of freedom. age: 41. Statistical analysis The study was approved by the Ethical Committee at the Chang. In addition. and 1 U Hotstar Taq polymerase (Qiagen Han population. Systemic Lupus Erythematosus Disease Activity Index. Direct sequencing was analyzed by the ABI 3730XL DNA relevant to RA and SLE in the Chinese Han population. Anti-double-stranded DNA.% 292/677 (43. 1 ll 1" PCR our previous study [11]. Subjects and methods assignment was successful in >98% of samples tested. Rheumatoid fac- (Lyp). 1 ll primer mix cantly associated with ankylosing spondylitis (AS) in the Chinese (1 lM each primer). PTPN22 polymorphisms. USA) in a total volume of 10 ll.3 Sm+.6 ± 13. ican white population [10]. Sample collection 2. SLE control: R620W and systemic lupus erythematosus (SLE) in a North Amer.3 RNP+. tion) 1987 revised criteria for RA [15] were recruited from the first receptor type 22 (PTPN22). were associated with the genetic susceptibility of systemic lupus erythematosus and rheumatoid arthritis in a Chinese Han population. showed an association between the PTPN22 for this study was also enrolled (RA control: 564.9%) 0/672(0%) ANA+. Together. ple autoimmune diseases (matched for ethnicity. ESR. systemic lupus erythematosus (SLE) [6] and (CRP).1 112 ± 14. For SLE. C-reactive protein. Ribonucleoprotein. Genotyping susceptibility to both systemic and organ-specific autoimmune diseases. single strand DNA-binding protein.2(22–77 years) 36.1. PLT. 72 "C for 1 min.% 436/674 (64.

11[0. Allelic analysis position of the SLE cohort revealed that the frequency of the rs3765598T was significantly higher in patients (17%) compared with controls (9.11 0.78 p < 0.43]).76].0002.68–1.65[0.9 (http://pngu.09–5. The allele frequency of rs2476601 in both RA and SLE cases and controls (RA vs.86e!009. were associated with the genetic susceptibility of systemic lupus erythematosus and rheumatoid arthritis in a Chinese Han population.usc. The corresponding ORs and 95% confidence intervals (CI) were assessed using a standard logistic regression analysis.5 (small effect size) using Quanto Powerc (http://hydra. dominant and reces- G G C C T T T sive models of rs3765598 were significant different in SLE and con- 1:114113273 1:114124709 1:114095139 1:114106505 1:114089610 1:114089190 1:114068705 trol(SLE: padd < 0.74.89] Genotype data for the 7 PTPN22 SNPs successfully typed in the Chinese Han cases (RA and SLE) and controls were examined by b OR(95% CI) single-marker analysis (Tables 2 and 3).68e!005.001 p = 0.77] 0. Bonferroni correction was applied to adjust the p value (Padj) in – multiple comparisons.48.54–0. 0.25 0. – p Control(freq. 2. Control(freq. / Human Immunology xxx (2016) xxx–xxx 3 assuming an odds ratio (OR) of 1.17 0. OR [95%CI] = 1.57e!008 4. RA and controls. Individual analyses of associations between PTPN22 polymor- Abbreviation: SNP. but not in RA (p > 0.12[0.1) or OR = 1.78] formed by comparing alleles in cases and controls using Fisher’s b OR(95% CI) exact test. PTPN22 polymorphisms. Statistical significance was set at 0.27 0. padj.01e!008 previous reports in Asians [11.74 0.0014).05. padj = 6.031 0.24 0. Single-locus association 84 85 85 74 61 50 1. padj < 0.) 3.52] 1.01e!008.edu/~purcell/plink/) 69 53 41 – [17]. rs3811021: 0.edu/gxe).004..095 0.1.48 0.mgh.76] 0.20].55–0. OR Minor allele [95%CI] = 0. controls: 0% vs.5.67e!005.0001. Please cite this article in press as: L. L.06[0. but not R620W.10 All variants in cases and controls were in Hardy-Weinberg equi- 0 librium (HWE) (p > 0.028 tion between the missense SNP (rs2476601.08%.006. Linkage disequilibrium (LD) analysis was 6.54] phisms and RA and SLE.17–0.26[0.1016/j. even after the Bonferroni’s p correction (RA: pdom < 0.07e!004 performed in RA and SLE patients using Haploview program [18].) padj = 2.58] 1. OR [95%CI] = 0. padj < 0. Case(freq.062 0. padj = 4.54– rs1217414 rs1217418 rs3765598 rs1746853 rs2476601 rs1970559 rs3811021 2. 95% CI.0001.42]. the distributions of additive.0008 The Bonferroni’s correction was carried out to adjust the p value.9 to 85 in RA population and from 41 to 0. Thus.70[0.71–1.0001.038 (SLE: pdom < 0.004 distribution of dominant model of rs1217414 were significant 0.86e!009 from further analysis. 0.57[0.42] 0.12[0.09 OR and 95% CI are calculated for the minor allele of each SNP.68e!006.5%) (p = 9. the distribution of dominant and recessive models of rs3811021 were significant different in SLE and control 0.20[0.028.65[0. Freq.24 0.2016.43–0. single nucleotide polymorphism. rs2476601 was omitted Allele distributions of PTPN22 gene polymorphisms in RA and SLE cases and healthy controls.24] 1. Systemic lupus erythematous. OR [95%CI] = 0. http://dx.038 0. but not in RA(p > 0.09–5. While.68e!006 each haplotype with the more common haplotype in the popula- tion using Fisher’s exact test.55–0.04.6 in SLE population (Table 2).042).17 0.10[0. padj < 0.26[0.2 using the PLINK 1.11 0.07e!004.0001.27 0.12[0. Tang et al.17 0.13 0.81–1.0001. The statistical analysis was performed 48.05[0.54–0.0001. 1.) study to detect association with those minor allele frequencies (MAFs) ranged from 48. Tang et al.05).1% vs.23 0.04 SLE 93. Rheumatoid arthritis.021 .doi.89]) and SLE 0. Immunol. padj = 0. OR.22 0.0001. In addition. but not for RA (Table 3).9 3. –.57e!008. SLE: p > 0.68e!005 6. rs3811021: p = 6.0001.6 86. odds ratio. Power calculations assume a = 0.38e!009.28 0.05 and small effect size (0.04 RA (rs1217414: p = 8.05).93–1.93[1. OR[95% – – – – – CI] = 1. padj = 6.31] 1. Results 0.57 0. Moreover.humimm.68 different in SLE.11 0.24].90–1.93[1.14 0.43–0. Table 2 which indicated that T allele in rs3765598 might revealed a strong a c b risk factor for SLE. OR [95%CI] = 1.54–2.) padj = 0.12 0. padj < 0.86–1. Genotype analysis showed that the 0. SLE vs. 95% confidence intervals. OR [95%CI] = 0.org/10. controls: 0.51] 1. SLE. not calculated.38e!009 6. SLE: pdom = 0.007).57[0. but did not differ significantly from that in RA cohort SNP ID (11%) and controls (9%) (p = 0.31] 1.43] 1.05).17–0.57 [0.67e!005 9. 0%) was much lower than that in Caucasian population (>8%) [19] and was similar with the 2. R620W) and neither a Padj RA nor SLE in the Chinese Han population (RA: p = 0.81–1. prec = 0. The results showed no associa- 0. padjusted. padj = 0.05).57[0. 0. the statistical power of the Case(freq.70[0. as well as autoantibody status were per- 0. pdom < 0.78]) were observed in further allelic analysis. Specific P values and – – – – ORs and 95% confidence intervals (CI) were obtained by comparing 8. 0 Powerc 48. prec = 0.2 93. frequency. Significant associations between rs1217414 and rs3811021 and RA (rs1217414: p = 2. Analysis of haplotype diversity was performed using the a padj expectation-maximization algorithm (EM).harvard. RA. padj = 0. (2016).52]).0008. Hum.12 0..95–1.

6. Systemic lupus erythematous.006 and the summary statistics r2 was calculated using the HaploView 0. But no associ- 4/99/461 0/43/512 0/1/563 ation between the functional rs2476601 polymorphism of the PTPN22 gene and susceptibility to RA and SLE was observed.(G) rs1970559. padj = 5.61.73e!016. OR[95%CI] = 0.39. padj = 1.02 -positive SLE group or clinical features -negative SLE group. Padjusted.21 [1.15– – – – – 2.18 0. 0.042 Pb(adj) 0. single nucleotide polymorphism.0008 model) 0.79–3.01 patients with SLE were genotyped for polymorphisms in the PTPN22 gene that was previously reported to be associated with Pa(Add P value were calculated using Fisher’s exact test. –. The data showed that two of the PTPN22 – – – – polymorphisms examined (rs1217414 and rs3811021) were signif- 24/316/224 39/183/342 4/112/448 5/158/401 Control(n) icantly associated with RA and SLE in our material. Seven haplotypes in RA and SLE separately. No significant evidence of association between the PTPN22 <0. odds ratio. 0.52 1. GCTTT: p = 3. 0. 1.(T) rs3765598.48 0. padj = 5.0001 polymorphisms and other clinical features. Furthermore. SLE.64 [1. Tang et al. 1. As to – – – – – stratification for ANA1 status in SLE.006. 0. Tang et al.92 program.07 – – – – – – In the current study. 0.14 1.40 [1. each with a fre- – – – quency >1%. OR <0.26e!006.0001 <0.(G) rs1746853.2016. 358 unrelated patients with RA and 713 Dominant model. not calculated.02 of allele frequencies of RF-positive and RF-negative revealed no Pa(Rec OR.063 Pb(adj) and SLE (ACGTC: p = 7.doi.74. Association of the PTPN22 polymorphisms with clinical features in RA and SLE 25/193/495 10/145/558 48/264/401 35/177/501 0/89/624 0/58/655 Regression analysis was also used to evaluate possible correla- 0/0/713 Case(n) tion between the PTPN22 risk alleles and the specific clinical and SLE serological features in RA and SLE shown in Table 5.11.org/10. ACPA-status was not known for RA patients in previous study.006 tus: RF-positive RA group and RF-negative RA group. autoimmune diseases.0001 [95%CI] = 2.02 0. Comparison 0. both Genome Wide Association Studies (GWAS) and Table 3 case-control studies indicated that PTPN22 is second in importance b a in autoimmune disorders.24.54. PTPN22 polymorphisms. Add model. Immunol. 1.53. 308 patients with – – – – – RF information available were divided into two groups by RF sta- model) 2. rs3765598 might revealed a strong risk factor for SLE.05 common haplotype with a frequency of approximately 65% in RA Pa(Dom and SLE.04.0002 model) 0.04.06–0.85e!004.humimm.51!015.0001 detected between rs3765598T and ANA1 status in ANA1-positive Distribution of the genotypes of PTPN22 gene polymorphisms in RA and SLE cases and controls. Haplotype analysis Abbreviation: SNP. 0.14 Among 358 patients with successful genotyping.0006. but not for RA. we observed marginally significant increase 1.94.021 . rs1746853.23e!007.0001 <0.(T) (minor allele) and laboratory parameters analyzed (except for rs3765598 and ANA 1 status in SLE).34]. rs.85 [1. were associated with the genetic susceptibility of systemic lupus erythematosus and rheumatoid arthritis in a Chinese Han population. was Pa(Dom detected.36 rection. The haplotype ACTTT was the most 0.9. GCTTT: <0. The PTPN22 gene. OR.12–3. OR [95%CI] = 1.55 0. 0.91.0001 <0.06 0.10]) and SLE(p = 8.(T) rs2476601.47.06. Recessive model. Padj. In addition.0001 for these 5 markers based on the haplotype block using PLINK 0. – rs1970559.44. SNPs.(C) rs1217414. no association was RA found between the seven PTPN22 SNPs and most of the clinical rs1217418. rs3765598.009 0. OR. Rec model.0014 Pb(adj) 0. 1 and 2). even after a Stringent Bonferroni cor- model) 0.16. 0.55. 0. 0.58.3. Please cite this article in press as: L.0001 p = 2.002– 1.65]) 0. Recently. / Human Immunology xxx (2016) xxx–xxx 3. Hum.47. OR[95%CI] – – – – – = 2.15 0. 0. model) 1. padj = 6.042 Pb(adj) 0. OR.4 L.007 Pairwise LD for the 6 PTPN22 SNPs (except for rs2476601) was – – – – – defined using the genotype data from RA and SLE cases separately.71. padj = 2. but not R620W. 1. OR[95%CI] = 0. OR.21]) (Table 4).74e!011. Pb(adj) 4.62e!005.11 – – – [0. in the distribution of haplotype ACGTC and GCTTT in RA (ACGTC: – p = 0. OR. (2016).29e!018.63].24.(C) rs3811021. Discussion 0.004. OR. significant differences between the two groups (p > 0. 0. – The Bonferroni’s correction was carried out to adjust the P value.79 0. Dom model. 0. 0. OR[95%CI] = 2. Pa(Rec 5.2. http://dx. haplotype ACTTC might define protective effect Pa(Add to RA(p = 7.43.1016/j.87]).0001 <0. Haplotypes were predicted <0. were predicted in both cases and controls accounting <0.80e!017. 95% confidence intervals. Additive model.02 [0.57–3. Moreover..74. Pb(adj) 0.05). Rheumatoid arthritis. 95% CI. 0.0001 for >95% of all the haplotypes. 0.93. Five SNPs (rs1217418. 33/297/342 50/226/396 6/127/539 6/174/482 4/121/547 Control(n) 0/52/620 0/0/672 3.81e!010. 0. con- firming the evidence that the PTPN22 rs2476601 may not predis- 31/130/197 12/101/245 pose individuals to the progress of RA and SLE in the Chinese 6/77/275 4/67/287 1/28/329 1/20/337 0/1/357 Case(n) Han cohorts.63[1.13. 0. either clinical features model) 0. 1. OR[95%CI] = 1.14 and ANA1-negative groups (p = 0.84 0.31]). 0. RA. rs3811021) were in one block in SLE and RA popula- – – tions (Supplementary Figs.58. Additionally. significant association was <0.29–2.81. padj = 0. 0. following the MHC.

52) 0. 1.91(0.85–1. Systemic lupus erythematous. Anti-double-stranded DNA. 95% CI.18.66 0.06 2.73e!016 5.35–1.05.29–2..01 0.86.93.35 [1.93(0.74.11[0.51!015 0. 5 .73–1.14(0.75–1. OR.08(0.93(0.90) rs3811021 0. rs3765598.002 0. not calculated.88–1.12 0.81e!010 2.humimm. single nucleotide polymorphism. 0. 1.64 0.87] GCGCT 0.62.99(0. P value were calculated using Fisher’s exact test.47–1. SNPs RA SLE RF(n = 308) But(n = 679) ANA1(n = 698) dsDNA(n = 674) Anti-Sm(n = 683) RNP(n = 677) Anti-SSB(n = 655) (pa.70–1.08 0.31) 0. 0. a The alleles were compared between the clinical features – positive group and clinical features – negative group.33) 0.18.26 – 0.98(0.72. antinuclear antibodies 1. 1.52) 0.25(0.66.42) 0.41) 0.01 – – – ACTTC 0.15] GCTTT 0.erythematosus and rheumatoid arthritis in a Chinese Han population.80e!017 0. Tang et al.11.05 – 0.72–1.78) 0.28) 0. were associated with the genetic susceptibility of systemic lupus Table 4 Haplotype analysis of RA and SLE cases and the healthy controls in the PTPN22 genes.41–1.21(0.21] ACTTT 0.23–0. OR 95%CI) (pa.07(0. Hum.63] ACGTC 0.61) 0.21 [1.56–1.79. RF.98) 0.003 1. 1.87) 0.52–1.72) 0.07 0.008 0.. 0.) Pb padjc OR[95%CI] ACGTC 0.22(0. RA.62e!005 1. RNP.65–1.03(0.23e!007 2.15) 0.75(0.85–1.63(1.32–2.69. 1.27) 0.74e!011 6. rs1746853.89–1.03 0.03 0.15–2.56) 0.70–2.11. 1. 0.12–3.91) rs1217418 0.63 0.36.10) 0. 1. 1. 1. rs1970559. 95%CI) (pa. RA SLE Haplotypea Case(freq.23.15. c The Bonferroni’s correction was carried out to adjust the p value.76–1. 95% confidence intervals.33(0.53–1.97) 0.00] ACTTT 0.29.87(0.65.55) 0.10(0.07 0.65.92(0.48–1.) Pb padjc OR[95%CI] Haplotypea Case(freq. 1. 0. Immunol. 1. single strand DNA-binding protein.79. PTPN22 polymorphisms.06(0.93.45–2. 0.34] ACGTT 0.) Control(freq.41) 0.37(0. 0.08] ATGTC 0. not calculated.68) 0. OR 95%CI) (pa.20. 0. frequency.doi.32.45) 0.63–1.82–1.39.44(0.06) rs3765598 0.85) Abbreviations: SNP.12–1. 0.53 [1.01 0.021 Please cite this article in press as: L.09 7.57–3. 0. Sm. odds ratio.56.06–0.49.67 0.38. 1.68–1. 0. http://dx. OR. b L. OR 95%CI) (pa.44) 0.24–1.84–1.33(0.25(0. 0. SSB. dsDNA. –.75–2.94–1. 1.62) 0.08 0. 0.77 – 0.85 [1. SLE. Freq.1016/j.74(0.22–4. Anti-Sm antibody.59(0. 1.92.02 7.01 0.75–1. –. OR 95%CI) (pa.56) 0. padjusted.12.65(0.95(0. Table 5 The association between clinical characteristics in SLE and RA and PTPN22 polymorphisms.08 0.88–1.96. 1. 0.90(0.09 8. RA.86) rs1970559 0. butterfly erythema. 1.21–1.79–3.81.10(0.24–2.90[0.69(0. OR 95%CI) (pa.21(0.71. Systemic lupus erythematous.04 2. odds ratio. 95% confidence intervals.72e!005 3.29(0.66–1.85e!004 2.0004 0.006.82 [0.11) 0. 1.002–0.90e!004 3. Rheumatoid arthritis.2016. a Haplotype structure of PTPN22 for RA and SLE were rs1217414.26e!006 2.64.65] GCTTT 0.40–2.04.) Control(freq.098 0. / Human Immunology xxx (2016) xxx–xxx P value were calculated using Fisher’s exact test.16(0. ANA1.29(0.35] ATGTC 0. Ribonucleoprotein.20) 0.50–2.77] ACGTT 0. 0. 0. 1. 0. 1. But. OR. OR 95%CI) rs1217414 0.75–1. Rheumatoid arthritis.42(0.59) 0. padj.0006 0.99–2. 1. 0.org/10.27–1.64) 0.10] ACTTC 0.67) 0. 1.45(0.49] GCGCT 0.29e!018 5.95 [0. but not R620W.43.17(0.014 – – – Abbreviation: SNP.64 [1.004 1.02 [0. rs3811021. 1.78(0.01) 0.41.28) 0. Tang et al.53) 0.25.15) 0.19(0. rs1217418.61–2. 95% CI. 1.69.68–1.01 5.056 0.66–1. single nucleotide polymorphism.72) rs1746853 0.20.40 [1. (2016).64[1.57(0.04 0.88) 0.03 3.83.03) 0. SLE. 1.77–1.08 0.39–1.03(0.38–1.10.16(0.76) 0. rheumatoid factor.26.83–6.

and SLE and RA after using Bonferroni’s correction. Appendix A. And. codes for the lymphoid specific tyrosine and rs3811021 in the development of immune-mediated diseases. Furthermore. Moreover. Similar results were reported by Lee et al. Hum. Immunol. ported our previous finding that conducted on Ankylosing ease in Caucasian [9].1016/j. The frequencies of the 1858T in not with RA.6 L. Carton Education Department of Hunan (15A023). and further study should be carried out to search for more sig- between this SNP and RA in UK [27] and Western Algerian [28]. were associated with the genetic susceptibility of systemic lupus erythematosus and rheumatoid arthritis in a Chinese Han population.humimm. phosphatase protein.43]. which sup- were strongly associated with rheumatoid factor–positive (RF) dis. but RA and SLE susceptibility locus. / Human Immunology xxx (2016) xxx–xxx located at chromosome 1 (1p13. the rs2476601 was reported to be lack 5. it may be linked to some as from north American [10] and Colombia [13]. (2016). Interesting. Supplementary data In addition. of RA and SLE separately. 08%) in the present study were much lower than rs3789604. These results suggested a potential role for rs1217414 linkage to RA and SLE. Similarly.1%) patients and controls (SLE controls: 0%. rs1746853. although the rs1217414 and rs3811021 may as Sweden [24]. The result in PTPN22 gene. functional polymorphisms in PTPN22 gene. Before the course of this work. In contrast with the studies above. firstly revealed a significant association between the SNP1 dation of Hunan Province (2015JJ6010) and the construct program (rs1217414) and SNP36 (rs3811021) and RA in two unrelated of the key discipline in Hunan province. but not R620W. the frequency of Our results show that two non-coding polymorphisms rs2476601 was 60. Colombian [13]. LYP was shown to interact with the neg. in non-coding region [44] and studies have suggested that many vation [21–23]. and rs3765598 might be a risk factor geneity between the Caucasian and Chinese Han populations from for SLE but not RA in Chinese Han population. Statistical association American [25]. PTPN22 C1858T has been now unanimously accepted as a Interesting. which was identified to be associated with autoim- those previously reported for a US-based Caucasian RA and SLE mune diseases. which disrupts the Lyp-Csk interaction and therefore results the intronic and 30 -UTR SNPs in the PTPN22 gene might affect the in autoimmune disorders. a significant association was found between rs1217414 and Type I psoriasis in UK [42]. the evidence that the PTPN22 1858T might not be the susceptible To evaluate the combined influence of multiple SNPs of the locus for SLE and RA in the Chinese Han population. as well as SLE in Supplementary data associated with this article can be found. Please cite this article in press as: L. observed between rs3811021 and RA in Caucasian populations 04.3) region which shows [36. no association was observed between PTPN22 side R620W is associated with human autoimmune diseases. splice processes of PTPN22. These observations indicated that phan. the need to further explore the primary association between Given the PTPN22 R620W was not polymorphic in the Chinese PTPN22 and autoimmune diseases. Moreover. Conclusions of polymorphism in Asian population including Chinese Han. National Science Foun- et al. Logistic regression analysis indicated Significant association was observed between the rs2476601 that haplotypes ACGTC and GCTTT significantly increase the risk and rheumatoid factor(RF) in RF-positive patients and healthy con. the susceptible TT and TC genotypes of PTPN22 rs2476601 rs1970559 and rs3811021 of PTPN22 with RA and SLE. GCTTT and ACTTC as the results reported in Japanese [29]. rs3765598 was found to be associated with SLE. bility of both SLE and RA. This was just a hypoth- growing bodies of studies have also shown significant association esis. It is unlikely that a single locus in the PTPN22 gene is solely responsible for the T cell dysfunction in autoimmune None. Lyp. This discrepancy may relate to different genetic back.humimm. association between haplotypes and SLE and RA present study was contrary to that in Caucasian in UK [27]. leading to aberrant expression of Associations between this polymorphism and SLE susceptibility PTPN22 and thereby influencing the susceptibility to autoimmune have been identified in different populations from European such diseases. Iranian [31]. disorders.02 and ground in sample selection. the Key Foundation of the vious findings in UK and European-American populations. Han population.doi. PTPN22 polymorphisms. Japanese. white North Americans populations [39]. The Foundation of the Educa- including SLE and RA.03) in Dutch population [36].1% in RA indicated that the rs2476601T carriers (rs1217414 and rs3811021) might decrease the genetic suscepti- were rare in this population. Tang et al. Genetic and environmental hetero. There are an increasing number of new pathogenic variants located ative regulatory kinase. And significant association was detected between this SLE (0%) and RA (0. Crete [12] and Polish [26].11 separately. which was confirmed by a meta-analysis study and a case-control study later [40. Never the less. further [37] and Helen et al.doi. rant splice processes [45–47]. sion analysis indicated that Haplotype ACTTC may significantly sian [35]. which highlighted which the RA cohorts might explain the inconsistency. Spanish [25]. Indian [30]. In our study. Logistic regres- Turkey [32]. thereby inhibiting T lymphocyte acti. And. Tang et al. it is a matter of debate whether the rs2476601 polymorphism is the only PTPN22 disease-associated variant in Conflict of interest Asian populations. tion Department of Hunan (15C0513). Thus. Egyptian [33]. nificant evidence.org/10. Spanish [34] and Rus.41]. but the same was detected between the haplotype ACGTC. rs3765598. similar studies have suggested statistically significant associations between the two We are grateful to the SLE and RA patients and control individ- SNPs (rs1217414 and rs3811021) and autoimmune disorders uals for participating in this study. African was also analyzed in the current study.org/10. 0. a significant association was detected between an intron polymorphism (rs1217414) and ankylosing spondylitis (AS) in the Chinese Han Acknowledgements population.04.021 . 1858C > T) in the PTPN22 disease-related non-coding region SNPs are responsible for aber- gene encodes the amino acid substitution of arginine to trypto. Indian and Iranian et al. Csk. between haplotypes containing rs1217418. This discovery support that other SNP in 30 UTR out- cohorts [9]. in European-Americans [25]. locus and ANA1 in SLE as well.2016. Thus. The results of this study supported the pre.1–1p13. as well not have any functional significance itself. http://dx. at http://dx. spondylitis in Chinese Han population [11]. 1858T and neither SLE nor RA in our samples. decrease the risk of RA and SLE with odds ratio equal to 0.021.2016. As reported in our previous study [11]. Rs3765598 is absolute LD with RA controls: 0..55 (p = 0. presence of rheumatoid factor–positive disease in Spanish RA patients [14].1016/j. This is the first report on the association trol with an OR equal to 1. protective effect was also the online version. no investigation with a larger sample size and haplotype analysis with association was found between the PTPN22 rs2476601 and the more SNPs should be required to confirm the present result. A mutation (rs2476601. Western Algerian [28] and Crete [12]. which supports the function of this SNP is still hardly known. [38].

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